We examined the relative roles of contemporary (species interactions) and historical factors (phylogeny) in structuring a lizard assemblage (14 species) from one of the last remaining large expanses of undisturbed Cerrado in Brazil. Niche breadth for microhabitat was low for all species in the assemblage, and microhabitat niche overlaps varied from none to almost complete and appeared associated with phylogenetic similarity. Mean microhabitat and diet overlaps among lizard species did not differ statistically from random, based on a pseudocommunity analysis, indicating a negligible role of contemporary factors in assemblage structure. Prey overlaps were highest within Gymnophthalmidae and Teiidae. A cluster analysis of principal component scores of morphometric variables revealed groups corresponding to lizard families, suggesting a strong association between morphology and phylogeny. Similarities among closely related species in microhabitat use, diel activity, and diet breadth, based on cladogram inspection, suggested that phylogeny might affect assemblage structure. However, a Canonical Phylogenetic Ordination (CPO) analysis revealed no significant phylogenetic effects on lizard microhabitat use or diet composition. We suggest that under-representation of species in major clades (low taxon sampling) renders it difficult to detect potential historical and ecological effects on assemblage structure.